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Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae
M. Klumplerova, P. Splichalova, J. Oppelt, J. Futas, A. Kohutova, P. Musilova, S. Kubickova, R. Vodicka, L. Orlando, P. Horin
Jazyk angličtina Země Velká Británie
Typ dokumentu časopisecké články
Grantová podpora
CZ.1.05/1.1.00/02.0068
Central European Institute of Technology CEITEC
NPU LQ1601
Czech National Sustainability Programme
BioMedCentral Open Access od 2000
Directory of Open Access Journals od 2000
Free Medical Journals od 2000
PubMed Central od 2000
Europe PubMed Central od 2000 do 2020
ProQuest Central od 2009-01-01
Open Access Digital Library od 2000-07-01
Open Access Digital Library od 2000-01-01
Open Access Digital Library od 2000-01-01
Medline Complete (EBSCOhost) od 2000-01-01
Health & Medicine (ProQuest) od 2009-01-01
Springer Journals Complete - Open Access od 2000-12-01
Springer Nature OA/Free Journals od 2000-12-01
Odkazy
PubMed
32998693
DOI
10.1186/s12864-020-07089-6
Knihovny.cz E-zdroje
- MeSH
- Equidae klasifikace genetika MeSH
- fylogeneze MeSH
- hlavní histokompatibilní komplex genetika MeSH
- molekulární evoluce * MeSH
- polymorfismus genetický * MeSH
- rekombinace genetická MeSH
- selekce (genetika) * MeSH
- vznik druhů (genetika) MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family Equidae includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II DRA and DQA loci have received attention, the genetic diversity and effects of selection on DRB and DQB loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II DRB and DQB loci in the Equidae family. RESULTS: Three DRB and two DQB genes were identified in the genomes of all equids. The genes DRB2, DRB3 and DQB3 showed high sequence conservation, while polymorphisms were more frequent at DRB1 and DQB1 across all species analyzed. DQB2 was not found in the genome of the Asiatic asses Equus hemionus kulan and E. h. onager. The bioinformatic analysis of non-zero-coverage-bases of DRB and DQB genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for DRB1, DRB2, DQB1 and DQB2 genes. Trans-species allele sharing was identified in all genes except DRB1. Site-specific selection analysis predicted genes evolving under positive selection both at DRB and DQB loci. No selected amino acid sites were identified in DQB3. CONCLUSIONS: The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II DRB/DQB sub-regions in the Equidae.
Ceitec MU Masaryk University Kamenice 753 5 625 00 Brno Czech Republic
Ceitec VFU RG Animal Immunogenomics Brno Czech Republic
Ceitec VRI RG Animal Cytogenomics Brno Czech Republic
Centre for GeoGenetics Natural History Museum of Denmark Øster Voldgade 5 7 1350K Copenhagen Denmark
Department of Animal Genetics Veterinary and Pharmaceutical University Brno Czech Republic
Zoo Prague U Trojského zámku 120 3 171 00 Praha 7 Czech Republic
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- $a Klumplerova, Marie $u Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic $u Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
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- $a BACKGROUND: The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family Equidae includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II DRA and DQA loci have received attention, the genetic diversity and effects of selection on DRB and DQB loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II DRB and DQB loci in the Equidae family. RESULTS: Three DRB and two DQB genes were identified in the genomes of all equids. The genes DRB2, DRB3 and DQB3 showed high sequence conservation, while polymorphisms were more frequent at DRB1 and DQB1 across all species analyzed. DQB2 was not found in the genome of the Asiatic asses Equus hemionus kulan and E. h. onager. The bioinformatic analysis of non-zero-coverage-bases of DRB and DQB genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for DRB1, DRB2, DQB1 and DQB2 genes. Trans-species allele sharing was identified in all genes except DRB1. Site-specific selection analysis predicted genes evolving under positive selection both at DRB and DQB loci. No selected amino acid sites were identified in DQB3. CONCLUSIONS: The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II DRB/DQB sub-regions in the Equidae.
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- $a Horin, Petr $u Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic. horin@dior.ics.muni.cz $u Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic. horin@dior.ics.muni.cz
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